Scientia Agricultura Sinica ›› 2014, Vol. 47 ›› Issue (3): 564-573.doi: 10.3864/j.issn.0578-1752.2014.03.016


Genome-Wide Association Analyses for Musle pH 72 h Value and Meat Color Traits in Sutai Pigs

 ZHOU  Li-Sheng, YANG  Jie, LIU  Xian-Xian, ZHANG  Zhi-Yan, YANG  Bin, MA  Jun-Wu   

  1. Candidate of National Key Laboratory for Animal Biotechnology, Jiangxi Agricultural University, Nanchang 330045
  • Received:2013-04-23 Online:2014-02-01 Published:2013-09-18

Abstract: 【Objective】 The objective of this study is to identify candidate genes and molecular markers associated with meat quality traits of Sutai pigs. 【Method】 Genome-wide association analysis was conducted by using Illumina 60K SNP Bead-chip genotypes of 150 Sutai pigs. Phenotypic data of each animal included postmortem 72 h muscle pH(pH 72 h), pH drop from postmortem 45 min to 72 h (pHdrop_45 min_72 h), 72 h Minolta a, b, L (ColorM_a72 h, ColorM_b72 h, ColorM_L72 h) and subjective color score (ColorScore_72 h) of longissimus dorsi (LM) and semimembranosus (SM) muscle. Quality control was carried out using PLINK v1.07. SNP markers were removed if they had genotype-missing rates > 0.03 or minor allele frequencies (MAF) < 0.05 or Hardy-Weinherg P≤10-5. Samples were removed on low (<90%) call rate. After the quality control, all 150 samples passed the filter and a final set of 43 760 SNPs were selected for GWAS. The association analyses were conducted using GenABEL in the R software. SNPs were individually tested for association with all studied traits using a generalized linear mixed model and the genome-wide significance threshold was determined by the Bonferroni method. The influence of population stratification was assessed by examining the distribution of test statistics generated from the thousands of association tests and assessing their deviation from the null distribution in a quantile-quantile (Q-Q) plot. 【Result】 The relationship between LM_pH72 h and SM_pH72 h, between LM_pHdrop_45 min_72 h and SM_pHdrop_45 min_72 h, between LM_ColorM_b72 h and SM_ColorM_b72 h, between LM_ColorM_L72 h and LM_ColorScore_72 h and between SM_ColorM_L72 h and SM_ColorScore_72 h were significant (P < 0.05). There was no clear overall systematic bias in all studied traits and no very strong stratification existed. In total, 39 SNPs reached Bonferroni chromosome-wise significance and fell into 20 genomic regions of approximately 10 Mb or less. Among them, 17 SNPs significantly associated with pH values were detected on the chromosomes 3, 4, 10, 14 and X, except one unmapped SNP ASGA0082337. Other 22 SNPs for meat color located on the chromosomes 1, 3, 7, 10, 12, 14 and 15. The SNPs related to LM_ColorM_a72 h, LM_ColorM_L72 h, LM_ColorScore_72 h, SM_ColorM_L72 h and SM_ColorScore_72 h were not detected. Two SNPs M1GA0020074 and MARC0028756 on the chromosome 14 were significantly associated with pHdrop_45 min_72 h in both LM and SM. Linkage disequilibrium (LD) analysis by using Haploview version 4.2 software showed that M1GA0020074 and MARC0028756 were in a haplotype block spanning 433 kb.【Conclusion】The loci on SSC10, SSC14 and SSC15 appeared to have pleiotropic effects on several traits. BNIP3, PRKG1, ADRB3 and other genes near the significant SNPs are candidate genes for these traits and merit further validation.

Key words: GWAS , meat quality traits , pH , meat color , pig

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